Variant report

Variant	rs9524568
Chromosome Location	chr13:95279505-95279506
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1341267	0.97[ASN][1000 genomes]
rs1572935	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2298055	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2298056	0.97[ASN][1000 genomes]
rs2298057	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35253817	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3897473	0.89[ASN][1000 genomes]
rs3897474	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4238308	0.90[ASN][1000 genomes]
rs4296139	0.90[ASN][1000 genomes]
rs4465476	0.96[ASN][1000 genomes]
rs4771890	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492720	0.88[ASN][1000 genomes]
rs6492721	0.89[ASN][1000 genomes]
rs6492723	0.90[ASN][1000 genomes]
rs6492725	0.97[ASN][1000 genomes]
rs7326576	0.97[ASN][1000 genomes]
rs7981788	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9516445	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9516448	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9516450	0.90[AMR][1000 genomes]
rs9524555	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9524556	0.91[ASN][1000 genomes]
rs9524557	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9524559	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9524560	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9524561	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9524562	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9524563	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9524566	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556405	0.86[ASN][1000 genomes]
rs9561643	0.82[ASN][1000 genomes]
rs9561645	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9524568	GPR180	cis	lung	GTEx
rs9524568	GPR180	cis	Muscle Skeletal	GTEx
rs9524568	GPR180	cis	Nerve Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95254600-95284000	Weak transcription	Spleen	Spleen
2	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:95255000-95281000	Weak transcription	Colonic Mucosa	Colon
4	chr13:95255200-95282200	Weak transcription	Brain Angular Gyrus	brain
5	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr13:95255600-95281800	Weak transcription	Fetal Brain Male	brain
7	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
8	chr13:95255800-95284000	Weak transcription	K562	blood
9	chr13:95255800-95285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr13:95259800-95282000	Weak transcription	Brain Germinal Matrix	brain
11	chr13:95260000-95285800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:95264000-95284000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr13:95264200-95280200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr13:95264200-95299600	Weak transcription	Psoas Muscle	Psoas
15	chr13:95264600-95282400	Weak transcription	Pancreas	Pancrea
16	chr13:95264600-95289200	Weak transcription	Esophagus	oesophagus
17	chr13:95264600-95289600	Weak transcription	Fetal Kidney	kidney
18	chr13:95264800-95284600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr13:95265400-95286800	Weak transcription	A549	lung
20	chr13:95265600-95293400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:95268600-95281000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr13:95268800-95279600	Weak transcription	HUVEC	blood vessel
23	chr13:95268800-95283800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr13:95270000-95283400	Strong transcription	Dnd41	blood
25	chr13:95270400-95283400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr13:95270800-95283200	Strong transcription	Osteobl	bone
27	chr13:95271000-95280600	Strong transcription	Liver	Liver
28	chr13:95271000-95281200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr13:95271000-95283000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr13:95271000-95283600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:95271400-95282200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr13:95271600-95281800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr13:95272400-95282800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr13:95272600-95283400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr13:95274000-95284400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr13:95274800-95280200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr13:95275200-95280600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr13:95275200-95281200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:95275200-95282600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:95275200-95284000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr13:95275400-95280400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr13:95275400-95280600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr13:95275400-95282400	Strong transcription	HMEC	breast
44	chr13:95275400-95283000	Strong transcription	NH-A	brain
45	chr13:95275400-95283200	Strong transcription	Fetal Thymus	thymus
46	chr13:95275400-95283400	Strong transcription	Adipose Nuclei	Adipose
47	chr13:95275800-95288800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr13:95276200-95280400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr13:95276600-95292800	Weak transcription	Colon Smooth Muscle	Colon
50	chr13:95276600-95293600	Weak transcription	HSMMtube	muscle

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